The symbiotic gut bacteria of fish: dynamics of diet, physiology, and the environment

Karen Elizabeth Sullam

doi:10.17918/etd-7068

The ability for an organism to extract energy from its environment is central to its survival, reproduction and fitness. In addition to traits within the host that directly influence digestion, such as intestinal physiology and morphology, an animal's gut bacterial constituents can also strongly influence its digestive capabilities. In fact, bacterial communities that live in and on an organism can strongly influence the host's condition and fitness. Although fish are the most diverse vertebrate group, little is known about their microbial constituents or how they impact their physiology, ecology and evolution, and likewise, how fish affect the bacteria in their environment. To explore factors that shape fish bacterial communities, I investigated the variation in gut bacteria across fish species and populations. Through a meta-analysis of gut bacteria from diverse fish hosts, patterns of variation in response to alterations in diet, trophic level, and habitat were apparent from the 18 fish species included in the analysis. After focusing on a broad array of fish taxa, I concentrated on the Trinidadian guppy, Poecilia reticulata, which serves as a model system for evolutionary biology. I investigated the composition of guppy gut microbial communities as well as other elements of their digestive physiology that may affect their ability to extract energy from their environment. Through field surveys and a dietary manipulation, I found that populations of guppies differ in digestive traits, including digestive enzymatic profiles and gut morphology. The bacterial communities in guppies appeared to be largely divided by stream of origin, but because bacteria found in guppy guts were distinct from the bacteria in their environment, they appear to be driven, in part, by guppy population background. Finally, I expanded my investigation to examine how fish influence the community structure of bacteria in their environment. Using the threespine stickleback (Gasterosteus aculeatus) from lake and stream habitats in Switzerland, I explored how their presence and population background affect the structure of the bacterial communities in their experimental mesocosms. I also explored whether the effect of population background on environmental bacterial community structure is subject to plasticity due to the diet upon which they were reared. I found that the presence of fish strongly shapes the microbes that are present in their environment as well as their abundance. Additionally, the interaction of rearing diet and fish population background can also influence bacteria present in the mesocosms. The results from this dissertation show how fish ecology and environmental factors interact to shape the communities of gut bacteria in fish, and how fish can also influence the bacteria in their environment. This work is a key step to establish how bacterial communities are structured in fish and in their aquatic environments. It also lays the groundwork for future studies on the functional contributions of bacteria to fish ecology, which should lead to a better understanding of how fish interact with their environments.

The symbiotic gut bacteria of fish: dynamics of diet, physiology, and the environment

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The symbiotic gut bacteria of fish: dynamics of diet, physiology, and the environment

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